diff --git a/packages/dotagents/src/plugins/store.test.ts b/packages/dotagents/src/plugins/store.test.ts
index 47100dc..7dd591c 100644
--- a/packages/dotagents/src/plugins/store.test.ts
+++ b/packages/dotagents/src/plugins/store.test.ts
@@ -464,6 +464,54 @@ describe("plugin store", () => {
     }
   });
 
+  it("records every native fallback manifest when no root plugin.json exists", async () => {
+    const projectRoot = await mkdtemp(join(tmpdir(), "dotagents-plugin-dual-native-"));
+    try {
+      const sourceRoot = join(projectRoot, "source");
+      const pluginsDir = join(projectRoot, "installed");
+      await mkdir(join(sourceRoot, ".codex-plugin"), { recursive: true });
+      await mkdir(join(sourceRoot, ".claude-plugin"), { recursive: true });
+      await mkdir(pluginsDir, { recursive: true });
+      await writeFile(
+        join(sourceRoot, ".codex-plugin", "plugin.json"),
+        JSON.stringify({ name: "dual-tools" }),
+      );
+      await writeFile(
+        join(sourceRoot, ".claude-plugin", "plugin.json"),
+        JSON.stringify({ name: "dual-tools" }),
+      );
+
+      const candidates = await discoverPlugins(sourceRoot);
+      expect(candidates).toHaveLength(1);
+      expect(candidates[0]!.nativeSource).toBe("codex");
+      expect(candidates[0]!.authoredNativeInterfaces.codex?.fallback).toBe(true);
+      expect(candidates[0]!.authoredNativeInterfaces.claude?.fallback).toBe(true);
+
+      const resolved = await resolvePlugin(
+        { name: "dual-tools", source: "path:source" },
+        { stateDir: join(projectRoot, "state"), projectRoot },
+      );
+      const prepared = preparePluginForTargets(resolved.plugin, ["claude", "codex"]);
+      const installed = await installPluginBundle(pluginsDir, {
+        ...resolved,
+        plugin: prepared,
+      });
+      expect(installed.authoredNativeInterfaces?.claude?.fallback).toBe(true);
+
+      const reloaded = await loadInstalledPlugins(
+        pluginsDir,
+        [{ name: "dual-tools", source: "path:source" }],
+        "dotagents install",
+        ["claude", "codex"],
+      );
+      expect(reloaded.issues).toEqual([]);
+      expect(reloaded.plugins).toHaveLength(1);
+      expect(reloaded.plugins[0]!.authoredNativeInterfaces?.claude?.fallback).toBe(true);
+    } finally {
+      await rm(projectRoot, { recursive: true, force: true });
+    }
+  });
+
   it("rejects a .github Copilot manifest when a native fallback was imported", async () => {
     const projectRoot = await mkdtemp(join(tmpdir(), "dotagents-plugin-copilot-precedence-"));
     try {
diff --git a/packages/dotagents/src/plugins/store.ts b/packages/dotagents/src/plugins/store.ts
index 5e75dfd..d2e355e 100644
--- a/packages/dotagents/src/plugins/store.ts
+++ b/packages/dotagents/src/plugins/store.ts
@@ -905,7 +905,10 @@ async function loadPluginInterfaces(
     throw new Error("Installed plugin bundle is missing plugin.json. Reinstall the plugin.");
   }
 
+  let primary: { manifest: PluginManifest; nativeSource?: NativePluginSource } | undefined;
+  const authoredNativeInterfaces: AuthoredNativePluginInterfaces = {};
   for (const candidate of FALLBACK_MANIFEST_PATHS) {
+    if (primary && !candidate.nativeSource) {continue;}
     const filePath = join(pluginDir, candidate.path);
     if (!existsSync(filePath)) {continue;}
     const value = await readJson(filePath);
@@ -915,7 +918,7 @@ async function loadPluginInterfaces(
     } catch (err) {
       throw pluginManifestError(err, value);
     }
-    const authoredNativeInterfaces: AuthoredNativePluginInterfaces = {};
+    primary ??= { manifest, nativeSource: candidate.nativeSource };
     if (candidate.nativeSource) {
       authoredNativeInterfaces[candidate.nativeSource] = {
         path: candidate.path,
@@ -923,13 +926,13 @@ async function loadPluginInterfaces(
         manifest,
       };
     }
-    return {
-      manifest,
-      authoredNativeInterfaces,
-      nativeSource: candidate.nativeSource,
-    };
   }
-  return null;
+  if (!primary) {return null;}
+  return {
+    manifest: primary.manifest,
+    authoredNativeInterfaces,
+    nativeSource: primary.nativeSource,
+  };
 }
 
 async function loadAuthoredNativeInterfaces(
@@ -1135,10 +1138,7 @@ async function readInstalledPluginProvenance(pluginDir: string): Promise<{
 }> {
   const fallbackSources = await readNativeFallbackSources(pluginDir);
   const nativeSource = await readNativeSourceMarker(pluginDir);
-  if (
-    fallbackSources && nativeSource &&
-    (fallbackSources.size !== 1 || !fallbackSources.has(nativeSource))
-  ) {
+  if (fallbackSources && nativeSource && !fallbackSources.has(nativeSource)) {
     throw new Error("Installed plugin has conflicting native interface provenance. Reinstall the plugin.");
   }
   return { fallbackSources, nativeSource };